Nah, I think the train station was just regular explosives. They also bombed the Grand Staircase and neither blast did much. Considering the huge area of effect all the other PULSEs had, there's no way the explosion would've been that short-ranged or weak enough for the exterior of the station to hold up. I doubt they've got one-and-done PULSEs whenever they want to blow stuff up. We also stole booms from their first factory, I doubt that was their entire stash.
As for all other PULSEs, I don't think we've seen all there have been, maybe we never will. Just like how we never would've known about that Abra PULSE had we shown up at their base at any other time, or how we found the Wasteland's PULSE waaaay after it did it's job.